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NM_001012614.2(CTBP1):c.-190T>G AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 14, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003709576.2

Allele description [Variation Report for NM_001012614.2(CTBP1):c.-190T>G]

NM_001012614.2(CTBP1):c.-190T>G

Genes:
LOC129991984:ATAC-STARR-seq lymphoblastoid silent region 15125 [Gene]
CTBP1:C-terminal binding protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4p16.3
Genomic location:
Preferred name:
NM_001012614.2(CTBP1):c.-190T>G
HGVS:
  • NC_000004.12:g.1248917A>C
  • NG_052824.1:g.6413T>G
  • NG_171430.1:g.109A>C
  • NM_001012614.2:c.-190T>GMANE SELECT
  • NM_001328.3:c.39T>G
  • NM_001377186.1:c.39T>G
  • NM_001377187.1:c.-190T>G
  • NM_001377189.1:c.-189+1243T>G
  • NM_001377190.1:c.-189+732T>G
  • NM_001377192.1:c.-189+1243T>G
  • NM_001377193.1:c.-189+732T>G
  • NP_001319.1:p.Leu13=
  • NP_001364115.1:p.Leu13=
  • NC_000004.11:g.1242705A>C
Molecular consequence:
  • NM_001012614.2:c.-190T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001377187.1:c.-190T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001377189.1:c.-189+1243T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377190.1:c.-189+732T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377192.1:c.-189+1243T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377193.1:c.-189+732T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001328.3:c.39T>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001377186.1:c.39T>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004472879Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 14, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004472879.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature in individuals affected with CTBP1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This sequence change affects codon 13 of the CTBP1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the CTBP1 protein. It affects a nucleotide within the consensus splice site. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024